X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Freleases.html;h=93c126781374f333b0988d7e5b4126cdc9f11816;hb=88761692019661894f3d5fa897cccc61c055f339;hp=f9c0190fdc7cc27cc5683ad404f4522178d54e96;hpb=1428fd7600665cc4dbd59945ef88bfc98fe6bd1a;p=jalview.git

diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index f9c0190..93c1267 100755
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -1,3 +1,4 @@
+
 <html>
 <!--
  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
@@ -51,17 +52,165 @@ li:before {
   </p>
   <table border="1">
     <tr>
-      <th nowrap><em>Release</em></th>
+      <th nowrap><a id="Jalview.$$Version-Rel$$"><em>Release</em></th>
       <th><em>New Features</em></th>
       <th><em>Issues Resolved</em></th>
     </tr>
     <tr>
       <td width="60" align="center" nowrap><strong><a
+          id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.5">.5</a><br />
+          <em>22/06/2021</em></strong></td>
+      <td align="left" valign="top"><em>Development</em>
+        <ul>
+          <li>Updated building instructions</li>
+        </ul></td>
+      <td>
+        <ul>
+          <li>
+            <!-- JAL-3840 -->Occupancy calculation is incorrect for
+            alignment columns with over -1+2^32 gaps (breaking filtering
+            and display)
+          </li>
+          <li>
+            <!-- JAL-3833 -->Caps on Hi-DPI scaling to prevent crazy
+            scale factors being set with buggy window-managers (linux
+            only)
+          </li>
+        </ul> <em>Development</em>
+        <ul>
+          <li>Fixed non-fatal gradle errors during build</li>
+        </ul>
+      </td>
+    </tr>
+    <tr>
+      <td width="60" align="center" nowrap><strong><a
+          id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.4">.4</a><br />
+          <em>09/03/2021</em></strong></td>
+      <td align="left" valign="top"><em>Improved control of
+          Jalview's use of network services via jalview_properties</em>
+        <ul>
+          <li>
+            <!-- JAL-3814 -->New .jalview_properties token controlling
+            launch of the news browser (like -nonews argument)
+          </li>
+          <li>
+            <!-- JAL-3813 -->New .jalview_properties token controlling
+            download of linkout URLs from
+            www.jalview.org/services/identifiers
+          </li>
+          <li>
+            <!-- JAL-3812 -->New .jalview_properties token controlling
+            download of BIOJSHTML templates
+          </li>
+          <li>
+            <!-- JAL-3811 -->New 'Discover Web Services' option to
+            trigger a one off JABAWS discovery if autodiscovery was
+            disabled
+          </li>
+        </ul></td>
+      <td align="left" valign="top">
+        <ul>
+          <li>
+            <!-- JAL-3818 -->Intermittent deadlock opening structure in
+            Jmol
+          </li>
+        </ul> <em>New Known defects</em>
+        <ul>
+          <li>
+            <!-- JAL-3705 -->Protein Cross-Refs for Gene Sequence not
+            always restored from project (since 2.10.3)
+          </li>
+          <li>
+            <!-- JAL-3806 -->Selections from tree built from CDS aren't
+            propagated to Protein alignment (since 2.11.1.3)
+          </li>
+        </ul>
+      </td>
+    </tr>
+    <tr>
+      <td width="60" align="center" nowrap><strong><a
+          id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.3">.3</a><br />
+          <em>29/10/2020</em></strong></td>
+      <td align="left" valign="top">
+        <ul>
+
+        </ul>
+      </td>
+      <td align="left" valign="top">
+        <ul>
+          <li>
+            <!-- JAL-3765 -->Find doesn't always highlight all matching
+            positions in a sequence (bug introduced in 2.11.1.2)
+          </li>
+          <li>
+            <!-- JAL-3760 -->Alignments containing one or more protein
+            sequences can be classed as nucleotide
+          </li>
+          <li>
+            <!-- JAL-3748 -->CDS alignment doesn't match original CDS
+            sequences after alignment of protein products (known defect
+            first reported for 2.11.1.0)
+          </li>
+          <li>
+            <!-- JAL-3725 -->No tooltip or popup menu for genomic
+            features outwith CDS shown overlaid on protein
+          </li>
+          <li>
+            <!-- JAL-3751 -->Overlapping CDS in ENA accessions are not
+            correctly mapped by Jalview (e.g. affects viral CDS with
+            ribosomal slippage, since 2.9.0)
+          </li>
+          <li>
+            <!-- JAL-3763 -->Spliced transcript CDS sequences don't show
+            CDS features
+          </li>
+          <li>
+            <!-- JAL-3700 -->Selections in CDS sequence panel don't
+            always select corresponding protein sequences
+          </li>
+          <li>
+            <!-- JAL-3759 --> <em>Make groups from selection</em> for a
+            column selection doesn't always ignore hidden columns
+          </li>
+        </ul> <em>Installer</em>
+        <ul>
+          <li>
+            <!-- JAL-3611 -->Space character in Jalview install path on
+            Windows prevents install4j launching getdown
+          </li>
+        </ul> <em>Development</em>
+        <ul>
+          <li>
+            <!-- JAL-3248 -->Fixed typos and specified compatible gradle
+            version numbers in doc/building.md
+          </li>
+        </ul>
+      </td>
+    </tr>
+    <tr>
+      <td width="60" align="center" nowrap><strong><a
+          id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.2">.2</a><br />
+          <em>25/09/2020</em></strong></td>
+      <td align="left" valign="top">
+        <ul>
+        </ul>
+      </td>
+      <td align="left" valign="top">
+        <ul>
+          <li>
+            <!-- JAL-3757 -->Fresh install of Jalview 2.11.1.1 reports
+            "Encountered problems opening
+            https://www.jalview.org/examples/exampleFile_2_7.jvp"
+          </li>
+        </ul>
+      </td>
+    </tr>
+    <tr>
+      <td width="60" align="center" nowrap><strong><a
           id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.1">.1</a><br />
-          <em>11/08/2020</em></strong></td>
+          <em>17/09/2020</em></strong></td>
       <td align="left" valign="top">
         <ul>
-          <!-- -->
           <li>
             <!-- JAL-3638 -->Shift+arrow keys navigate to next gap or
             residue in cursor mode
@@ -116,12 +265,18 @@ li:before {
           <li>
             <!-- JAL-3477 -->Improved built-in documentation and command
             line help for configuring Jalview's memory
-          </li>
+          </li>                   
         </ul>
       </td>
       <td align="left" valign="top">
         <ul>
           <li>
+            <!-- JAL-3691 -->Conservation and Quality tracks are shown
+            but not calculated and no protein or DNA score models are
+            available for tree/PCA calculation when launched with
+            Turkish language locale
+          </li>
+          <li>
             <!-- JAL-3493 -->Escape does not clear highlights on the
             alignment (Since Jalview 2.10.3)
           </li>
@@ -130,6 +285,10 @@ li:before {
             doesn't slide selected sequences, just sequence under cursor
           </li>
           <li>
+            <!-- JAL-3732 -->Alt+Up/Down in cursor mode doesn't move
+            sequence under the cursor
+          </li>
+          <li>
             <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
             multiple EMBL gene products shown forÂ a single contig
           </li>
@@ -163,6 +322,34 @@ li:before {
             <!-- JAL-3597 -->Resolved memory leaks in Tree and PCA
             panels, Alignment viewport and annotation renderer.
           </li>
+          <li>
+            <!-- JAL-3561 -->Jalview ignores file format parameter
+            specifying output format when exporting an alignment via the
+            command line
+          </li>
+          <li>
+            <!-- JAL-3667 -->Windows 10: For a minority of users, if
+            backups are not enabled, Jalview sometimes fails to
+            overwrite an existing file and raises a warning dialog. (in
+            2.11.0, and 2.11.1.0, the workaround is to try to save the
+            file again, and if that fails, delete the original file and
+            save in place.)
+          </li>
+          <li>
+            <!-- JAL-3750 -->Cannot process alignments from HTTPS urls
+            via command line
+          </li>
+          <li>
+            <!-- JAL-3741 -->References to http://www.jalview.org in
+            program and documentation
+          </li>
+        </ul> <em>Launching Jalview</em>
+        <ul>
+          <li>
+            <!-- JAL-3718 -->Jalview application fails when launched the
+            first time for a version that has different jars to the
+            previous launched version.
+          </li>
         </ul> <em>Developing Jalview</em>
         <ul>
           <li>
@@ -170,24 +357,41 @@ li:before {
             data, causing cloverReport gradle task to fail with an
             OutOfMemory error.
           </li>
+          <li>
+            <!-- JAL-3280 -->Migrated the Jalview Version Checker to
+            monitor the release channel
+          </li>
         </ul> <em>New Known defects</em>
         <ul>
           <li>
+            <!-- JAL-3748 -->CDS shown in result of submitting proteins
+            in a CDS/Protein alignment to a web service is wrong when
+            proteins share a common transcript sequence (e.g.
+            genome of RNA viruses)
+          </li>
+          <li>
             <!-- JAL-3576 -->Co-located features exported and re-imported
             are ordered differently when shown on alignment and in
             tooltips. (Also affects v2.11.1.0)
           </li>
           <li>
-            <!-- JAL-3667 -->Windows 10: For a minority of users, if
-            backups are not enabled, Jalview sometimes fails to
-            overwrite an existing file and raises a warning dialog.
-            Workaround is to try to save the file again, and if that
-            fails, delete the original file and save in place.
+            <!-- JAL-3702 -->Drag and drop of alignment file onto
+            alignment window when in a HiDPI scaled mode in Linux only
+            works for the top left quadrant of the alignment window
           </li>
           <li>
             <!-- JAL-3701 -->Stale build data in jalview standalone jar
             builds (only affects 2.11.1.1 branch)
           </li>
+          <li>
+            <!-- JAL-3127 -->Sequence ID colourscheme not re-applied
+            when alignment view restored from project (since Jalview 2.11.0)
+          </li>
+          <li>
+            <!-- JAL-3749 -->Duplicate CDS sequences are generated when
+            protein products for certain ENA records are repeatedly
+            shown via Calculate-&gt;Show Cross Refs
+          </li>
         </ul>
       </td>
     </tr>
